Antimicrobial agents

ABSTRACT

The application relates to antimicrobial agents against Gram-negative bacteria, in particular to fusion proteins composed of an enzyme having the activity of degrading the cell wall of Gram-negative bacteria and a peptide stretch fused to the enzyme at the N- or C-terminus, as well as pharmaceutical compositions comprising the same. Moreover, it relates to nucleic acid molecules encoding such a fusion protein, vectors comprising said nucleic acid molecules and host cells comprising either said nucleic acid molecules or said vectors. In addition, it relates to such a fusion protein for use as a medicament, in particular for the treatment or prevention of Gram-negative bacterial infections, as diagnostic means or as cosmetic substance. The application also relates to the treatment or prevention of Gram-negative bacterial contamination of foodstuff, of food processing equipment, of food processing plants, of surfaces coming into contact with foodstuff, of medical devices, of surfaces in hospitals and surgeries.

This application is a continuation of U.S. application Ser. No.14/535,457, now U.S. Pat. No. 10,137,175, filed Nov. 7, 2014, which is adivisional of U.S. application Ser. No. 13/380,312, now U.S. Pat. No.8,906,365, filed Mar. 9, 2012, as a national phase application under 35U.S.C. § 371 of International Application No. PCT/EP2010/059146 filedJun. 28, 2010, which claims priority to European Application No.09163953.4, filed on Jun. 26, 2009. The entire text of each of theabove-referenced disclosures is specifically incorporated herein byreference without disclaimer.

BACKGROUND OF THE INVENTION 1. Field of the Invention

The present invention relates to antimicrobial agents againstGram-negative bacteria, in particular to fusion proteins composed of anenzyme having the activity of degrading the cell wall of Gram-negativebacteria and an additional peptide stretch fused to the enzyme on the N-or C-terminus. Moreover, the present invention relates to nucleic acidmolecules encoding said fusion protein, vectors comprising said nucleicacid molecules and host cells comprising either said nucleic acidmolecules or said vectors. In addition, the present invention relates tosaid fusion protein for use as a medicament, in particular for thetreatment or prevention of Gram-negative bacterial infections, asdiagnostic means or as cosmetic substance. The present invention alsorelates to the treatment or prevention of Gram-negative bacterialcontamination of foodstuff, of food processing equipment, of foodprocessing plants, of surfaces coming into contact with foodstuff, ofmedical devices, of surfaces in hospitals and surgeries. Furthermore,the present invention relates to pharmaceutical or cosmetic compositionscomprising said fusion protein.

2. Description of Related Art

Gram-negative bacteria possess an outer membrane, with itscharacteristic asymmetric bilayer as a hallmark. The outer membranebilayer consists of an inner monolayer containing phospholipids(primarily phosphatidyl ethanolamine) and an outer monolayer that ismainly composed of a single glycolipid, lipopolysaccharide (LPS). Thereis an immense diversity of LPS structures in the bacterial kingdom andthe LPS structure may be modified in response to prevailingenvironmental conditions. The stability of the LPS layer and interactionbetween different LPS molecules is mainly achieved by the electrostaticinteraction of divalent ions (Mg²⁺, Ca²⁺) with the anionic components ofthe LPS molecule (phosphate groups in the lipid A and the inner core andcarboxyl groups of KDO). Furthermore, the dense and ordered packing ofthe hydrophobic moiety of lipid A, favored by the absence of unsaturatedfatty acids, forms a rigid structure with high viscosity. This makes itless permeable for lipophilic molecules and confers additional stabilityto the outer membrane (OM).

Various types of agents having bactericidal or bacteriostatic activityare known, e.g. antibiotics, endolysins, antimicrobial peptides anddefensins. Increasingly microbial resistance to antibiotics, however, iscreating difficulties in treating more and more infections caused bybacteria. Particular difficulties arise with infections caused byGram-negative bacteria like Pseudomonas aeruginosa andEnterobacteriaceae.

Endolysins are peptidoglycan hydrolases encoded by bacteriophages (orbacterial viruses). They are synthesized during late gene expression inthe lytic cycle of phage multiplication and mediate the release ofprogeny virions from infected cells through degradation of the bacterialpeptidoglycan. They are either β(1,4)-glycosylases (lysozymes),transglycosylases, amidases or endopeptidases. Antimicrobial applicationof endolysins was already suggested in 1991 by Gasson (GB2243611).Although the killing capacity of endolysins has been known for a longtime, the use of these enzymes as antibacterials was ignored due to thesuccess and dominance of antibiotics. Only after the appearance ofmultiple antibiotic resistant bacteria this simple concept of combatinghuman pathogens with endolysins received interest. A compelling need todevelop totally new classes of antibacterial agents emerged andendolysins used as ‘enzybiotics’—a hybrid term of ‘enzymes’ and‘antibiotics’—perfectly met this need. In 2001, Fischetti and coworkersdemonstrated for the first time the therapeutic potential ofbacteriophage Cl endolysin towards group A streptococci (Nelson et al.,2001). Since then many publications have established endolysins as anattractive and complementary alternative to control bacterialinfections, particularly by Gram positive bacteria. Subsequentlydifferent endolysins against other Gram positive pathogens such asStreptococcus pneumoniae (Loeffler et al., 2001), Bacillus anthracis(Schuch et al., 2002), S. agalactiae (Cheng et al., 2005) andStaphylococcus aureus (Rashel et al, 2007) have proven their efficacy asenzybiotics. Nowadays, the most important challenge of endolysin therapylies in the insensitivity of Gram-negative bacteria towards theexogenous action of endolysins, since the outer membrane shields theaccess of endolysins from the peptidoglycan. This currently prevents theexpansion of the range of effective endolysins to importantGram-negative pathogens.

Antimicrobial peptides (AMPs) represent a wide range of short, cationic,gene encoded peptide antibiotics that can be found in virtually everyorganism. Different AMPs display different properties, and many peptidesin this class are being intensively researched not only as antibiotics,but also as templates for cell penetrating peptides. Despite sharing afew common features (e.g., cationicity, amphipathicity and short size),AMP sequences vary greatly, and at least four structural groups(α-helical, β-sheet, extended and looped) have been proposed toaccommodate the diversity of the observed AMP conformations. Likewise,several modes of action as antibiotics have been proposed, and it wasshown e.g. that the primary target of many of these peptides is the cellmembrane whereas for other peptides the primary target is cytoplasmicinvasion and disruption of core metabolic functions. AMPs may becomeconcentrated enough to exhibit cooperative activity despite the absenceof specific target binding; for example, by forming a pore in themembrane, as is the case for most AMPs. However, this phenomenon hasonly been observed in model phospholipid bilayers, and in some cases,AMP concentrations in the membrane that were as high as one peptidemolecule per six phospholipid molecules were required for these eventsto occur. These concentrations are close to, if not at, full membranesaturation. As the minimum inhibitory concentration (MIC) for AMPs aretypically in the low micromolar range, scepticism has understandablyarisen regarding the relevance of these thresholds and their importancein vivo (Melo et al., Nature reviews, Microbiology, 2009, 245).

Defensins are a large family of small, cationic, cysteine- andarginine-rich antimicrobial peptides, found in both vertebrates andinvertebrates. Defensins are divided into five groups according to thespacing pattern of cysteines: plant, invertebrate, α-, β-, andθ-defensins. The latter three are mostly found in mammals. α-defensinsare proteins found in neutrophils and intestinal epithelia. β-defensinsare the most widely distributed and are secreted by leukocytes andepithelial cells of many kinds. θ-defensins have been rarely found sofar e.g. in leukocytes of rhesus macaques. Defensins are active againstbacteria, fungi and many enveloped and nonenveloped viruses. However,the concentrations needed for efficient killing of bacteria are mostlyhigh, i.e. in the μ-molar range. Activity of many peptides may belimited in presence of physiological salt conditions, divalent cationsand serum. Depending on the content of hydrophobic amino acid residuesDefensins also show haemolytic activity.

SUMMARY OF THE INVENTION

Thus, there is a need for new antimicrobial agents.

This object is solved by the subject matter defined in the claims.

The term “protein” as used herein refers synonymously to the term“polypeptide”. The term “protein” as used herein refers to a linearpolymer of amino acid residues linked by peptide bonds in a specificsequence. The amino-acid residues of a protein may be modified by e.g.covalent attachments of various groups such as carbohydrates andphosphate. Other substances may be more loosely associated with thepolypeptide chains, such as heme or lipid, giving rise to the conjugatedproteins which are also comprised by the term “protein” as used herein.The various ways in which the polypeptide chains fold have beenelucidated, in particular with regard to the presence of alpha helicesand beta-pleated sheets. The term “protein” as used herein refers to allfour classes of proteins being all-alpha, all-beta, alpha/beta and alphaplus beta. Moreover, the term “protein” refers to a complex, wherein thecomplex refers to a homomer.

The term “fusion protein” as used herein refers to an expression productresulting from the fusion of two nucleic acid sequences. Such a proteinmay be produced, e.g., in recombinant DNA expression systems. Moreover,the term “fusion protein” as used herein refers to a fusion of a firstamino acid sequence as e.g. an enzyme, with a second or further aminoacid sequence. The second or further amino acid sequence may define adomain or any kind of peptide stretch. Preferably, said second and/orfurther amino acid sequence is foreign to and not substantiallyhomologous with any domain of the first amino acid sequence.

The term “peptide stretch” as used herein refers to any kind of peptidelinked to a protein such as an enzyme.

The term “peptide” as used herein refers to short polypeptidesconsisting of from about 2 to about 100 amino acid residues, morepreferably from about 4 to about 50 amino acid residues, more preferablyto about 5 to 30 amino acid residues, wherein the amino group of oneamino acid residue is linked to the carboxyl group of another amino acidresidue by a peptide bond. A peptide may have a specific function. Apeptide can be a naturally occurring peptide or a synthetically designedand produced peptide. The peptide can be, for example, derived orremoved from a native protein by enzymatic or chemical cleavage, or canbe prepared using conventional peptide synthesis techniques (e.g., solidphase synthesis) or molecular biology techniques (see Sambrook, J. etal., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press,Cold Spring Harbor, N.Y. (1989)). Examples of naturally occurringpeptides are antimicrobial peptides, defensins, sushi peptides. Examplesof synthetically produced peptides are polycationic, amphiphatic orhydrophobic peptides. A peptide in the meaning of the present inventiondoes not refer to His-tags, Strep-tags, thioredoxin or maltose bindingproteins (MBP) or the like, which are used to purify or locate proteins.

The term “endolysin” as used herein refers to an enzyme which issuitable to hydrolyse bacterial cell walls. “Endolysins” comprise of atleast one “enzymatically active domain” (EAD) having at least one of thefollowing activities: endopeptidase, chitinase, T4 like muraminidase,lambda like muraminidase, N-acetyl-muramoyl-L-alanine-amidase (amidase),muramoyl-L-alanine-amidase, muramidase, lytic transglycosylase (C),lytic transglycosylase (M), N-acetyl-muramidase,N-acetyl-glucosaminidase (lysozyme) or transglycosylases as e.g. KZ144and EL188. In addition, the endolysins may contain also regions whichare enzymatically inactive, and bind to the cell wall of the hostbacteria, the so-called CBDs (cell wall binding domains).

The term “EAD” as used herein refers to the enzymatically active domainof an endolysin. The EAD is responsible for hydrolysing bacterialpeptidoglycans. It exhibits at least one enzymatic activity of anendolysin. The EAD can also be composed of more than one enzymaticallyactive module.

The term “autolysins” refers to enzymes related to endolysins butencoded by bacteria and involved in e.g. cell division. An overview ofautolysins can be found in “Bacterial peptidoglycan (murein) hydrolases.Vollmer W, Joris B, Charlier P, Foster S. FEMS Microbiol Rev. 2008March; 32(2):259-86”.

The term “bacteriocin” as used herein refers to protein-like,polypeptide-like or peptide-like substances which are able to inhibitthe growth of other bacteria. Preferably said inhibition is specificallyby means of absorption of said other bacteria to specific receptors ofthe bacteriocin. In general, bacteriocins are produced bymicroorganisms. However, the term “bacteriocin” as used herein refersboth to an isolated form by a microorganism or to a syntheticallyproduced form, and refers also to variants which substantially retainthe activities of their parent bacteriocins, but whose sequences havebeen altered by insertion or deletion of one or more amino acidresidues.

The term, “antimicrobial peptide” (AMP) as used herein refers to anypeptide that has microbiocidal and/or microbiostatic activity. Thus, theterm “antimicrobial peptide” as used herein refers in particular to anypeptide having anti-bacterial, anti-fungal, anti-mycotic,anti-parasitic, anti-protozoal, anti-viral, anti-infectious,anti-infective and/or germicidal, algicidal, amoebicidal, microbiocidal,bacteriocidal, fungicidal, parasiticidal, protozoacidal, protozoicidalproperties.

The term “defensin” as used herein refers to a peptide present withinanimals, preferably mammals, more preferably humans, wherein thedefensin plays a role in the innate host defense system as thedestruction of foreign substances such as infectious bacteria and/orinfectious viruses and/or fungi. A defensin is a non-antibodymicrobicidal and/or tumoricidal protein, peptide or polypeptide.Examples for “defensins” are “mammalian defensins,” alpha-defensins,beta-defensins, indolicidin and magainins. The term “defensins” as usedherein refers both to an isolated form from animal cells or to asynthetically produced form, and refers also to variants whichsubstantially retain the cytotoxic activities of their parent proteins,but whose sequences have been altered by insertion or deletion of one ormore amino acid residues.

The term “sushi peptide” as used herein refers to complement controlproteins (CCP) having short consensus repeats. The sushi module of sushipeptides functions as a protein-protein interaction domain in manydifferent proteins. Peptides containing a Sushi domain have been shownto have antimicrobial activities.

As used herein, the term “cationic peptide” refers to a peptide havingpositively charged amino acid residues. Preferably a cationic peptidehas a pKa-value of 9.0 or greater. Typically, at least four of the aminoacid residues of the cationic peptide can be positively charged, forexample, lysine or arginine. “Positively charged” refers to the sidechains of the amino acid residues which have a net positive charge atabout physiological conditions. Examples of naturally occurring cationicpeptides which can be recombinantly produced are defensins, magainins,melittin and cecropins.

The term “polycationic peptide” as used herein refers to a syntheticallyproduced peptide composed of mostly lysine and/or arginine residues.

The term “amphipathic peptide” as used herein refers to peptides havingboth hydrophilic and hydrophobic functional groups. Preferably, the term“amphipathic peptide” as used herein refers to a peptide having adefined arrangement of hydrophilic and hydrophobic groups e.g.amphipatic peptides may be e.g. alpha helical, having predominantly nonpolar side chains along one side of the helix and polar residues alongthe remainder of its surface.

The term “hydrophobic group” as used herein refers to chemical groupssuch as amino acid side chains which are substantially water insoluble,but soluble in an oil phase, with the solubility in the oil phase beinghigher than that in water or in an aqueous phase. In water, amino acidshaving a hydrophobic side chain interact with one another to generate anonaqueous environment. Examples of amino acids with hydrophobic sidechains are alanine, valine, leucine, isoleucine, phenylalanine,histidine, tryptophane and tyrosine.

The term “deletion” as used herein refers to the removal of 1, 2, 3, 4,5 or more amino acid residues from the respective starting sequence.

The term “insertion” or “addition” as used herein refers to theinsertion or addition of 1, 2, 3, 4, 5 or more amino acid residues tothe respective starting sequence.

The term “substitution” as used herein refers to the exchange of anamino acid residue located at a certain position for a different one.

The present invention relates to new antibacterial agents againstGram-negative bacteria, in particular to fusion proteins composed of anenzyme having the activity of degrading the cell wall of Gram-negativebacteria and a peptide stretch fused to the enzyme on the N- orC-terminus or at both termini.

In one aspect of the present invention the enzyme having the activity ofdegrading the cell wall of Gram-negative bacteria is an endolysin,autolysin or bacteriocin.

In another aspect of the present invention the enzyme according to thepresent invention may further comprise regions which are enzymaticallyinactive, and bind to the cell wall of the host bacteria, the so-calledCBDs (cell wall binding domains).

Preferred fusion proteins according to the present invention aredepicted in SEQ ID NO:36 to 63. The fusion proteins according to SEQ IDNO:36 to 63 may comprise one or more additional amino acid residues onthe N-terminus. Preferably the additional amino acid residue ismethionine.

Preferably, the endolysin is encoded by bacteriophages specific forGram-negative bacteria such as Gram-negative bacteria of bacterialgroups, families, genera or species comprising strains pathogenic forhumans or animals like Enterobacteriaceae (Escherichia, especially E.coli, Salmonella, Shigella, Citrobacter, Edwardsiella, Enterobacter,Hafnia, Klebsiella, especially K. pneumoniae, Morganella, Proteus,Providencia, Serratia, Yersinia), Pseudomonadaceae (Pseudomonas,especially P. aeruginosa, Burkholderia, Stenotrophomonas, Shewanella,Sphingomonas, Comamonas), Neisseria, Moraxella, Vibrio, Aeromonas,Brucella, Francisella, Bordetella, Legionella, Bartonella, Coxiella,Haemophilus, Pasteurella, Mannheimia, Actinobacillus, Gardnerella,Spirochaetaceae (Treponema and Borrelia), Leptospiraceae, Campylobacter,Helicobacter, Spirillum, Streptobacillus, Bacteroidaceae (Bacteroides,Fusobacterium, Prevotella, Porphyromonas), Acinetobacter, especially A.baumanii.

Preferably, the autolysin is encoded by Gram-negative bacteria such asGram-negative bacteria of bacterial groups, families, genera or speciescomprising strains pathogenic for humans or animals likeEnterobacteriaceae (Escherichia, especially E. coli, Salmonella,Shigella, Citrobacter, Edwardsiella, Enterobacter, Hafnia, Klebsiella,especially K. pneumoniae, Morganella, Proteus, Providencia, Serratia,Yersinia), Pseudomonadaceae (Pseudomonas, especially P. aeruginosa,Burkholderia, Stenotrophomonas, Shewanella, Sphingomonas, Comamonas),Neisseria, Moraxella, Vibrio, Aeromonas, Brucella, Francisella,Bordetella, Legionella, Bartonella, Coxiella, Haemophilus, Pasteurella,Mannheimia, Actinobacillus, Gardnerella, Spirochaetaceae (Treponema andBorrelia), Leptospiraceae, Campylobacter, Helicobacter, Spirillum,Streptobacillus, Bacteroidaceae (Bacteroides, Fusobacterium, Prevotella,Porphyromonas), Acinetobacter, especially A. baumanii.

The bacteriocin is preferably specific for Gram-negative bacteria aslisted above, but may also be less specific.

The enzyme according to the present invention has cell wall degradingactivity against Gram-negative bacteria of bacterial groups, families,genera or species comprising strains pathogenic for humans or animalslike Enterobacteriaceae (Escherichia, especially E. coli, Salmonella,Shigella, Citrobacter, Edwardsiella, Enterobacter, Hafnia, Klebsiella,especially K. pneumoniae, Morganella, Proteus, Providencia, Serratia,Yersinia), Pseudomonadaceae (Pseudomonas, especially P. aeruginosa,Burkholderia, Stenotrophomonas, Shewanella, Sphingomonas, Comamonas),Neisseria, Moraxella, Vibrio, Aeromonas, Brucella, Francisella,Bordetella, Legionella, Bartonella, Coxiella, Haemophilus, Pasteurella,Mannheimia, Actinobacillus, Gardnerella, Spirochaetaceae (Treponema andBorrelia), Leptospiraceae, Campylobacter, Helicobacter, Spirillum,Streptobacillus, Bacteroidaceae (Bacteroides, Fusobacterium, Prevotella,Porphyromonas), Acinetobacter, especially A. baumanii.

Specific examples of an endolysin part derived from a phage or that is awild type endolysin are depicted in the following table:

TABLE 1 Wild type predicted function of phage publication endolysin theendolysin ΦV10 Perry, L. L. and Applegate, B. M. PhiV10p30 chitinaseFELS-1 McClelland, M. and Wilson, R. K. STM0907.Fels0 chitinase ε15Kropinksi, A. M. and McConnel, M. R. epsilon15p25 chitinase YUACeyssens. P. (Laboratory for Gene YuA20 lytic transglycosylase (C)/1technology) transmembranair domain (N) B3 Braid, M. D. and Kitts, C. L.ORF23 lytic transglycosylase (C)/2 transmembranair domains (N) BCEPμSummer, E. J. and Young, R. BcepMu22 lytic transglycosylase (M)/1transmembranair domain (N) F116 Byrne, M. and Kropinski, A. M. F116p62muraminidase (T4-like) FELS-2 McClelland, M. and Wilson, R. K.STM2715.S.Fels2 muraminidase (T4-like) ES18 Casjens, S. R. and Hendrix,R. W. gp76 muraminidase (T4-like) SETP3 De Lappe, N and Cormican, M.SPSV3_gp23 muraminidase (T4-like) ΦECO32 Savalia, D and Severinov, Kphi32_17 muraminidase (T4-like) HK022 Juhala, R and Hendrix, R. W.HK022p54 muraminidase (lambdalike) HK97 Juhala, R and Hendrix, R. W.HK97p58 muraminidase (lambdalike) HK620 Clark, A. J. and Dhillon, T. S.HK620p36 muraminidase (lambdalike) E1 Pickard, D. and Dougan, G VIP0007muraminidase (lambdalike) SF6 Casjens, S and Clark, A. J. Sf6p62muraminidase (lambdalike) SFV Allison, G. E. and Verma, N. K. R (SfVp40)muraminidase (lambdalike) BCEPC6B Summer, E J and Young, R. gp22muraminidase (lambdalike) BCEPNAZGUL Summer, E J and Young, R. Nazgul38muraminidase (lambdalike) P2 Christie, G. E. and Calender, R. K (P2p09)muraminidase (lambdalike) WΦ Christie, G. E. and Esposito, D. K (Wphi09)muraminidase (lambdalike) RV5 Kropinski, A. M. and Johnson rv5_gp085muraminidase (lambdalike) JS98 Zuber, S and Denou, E. EpJS98_gp116muraminidase (T4-like) 13A Savalia, D and Molineux, I. gp3.5muramoyl-L-alanine amidase BA14 Savalia, D and Molineux, I. gp3.5muramoyl-L-alanine amidase ECODS1 Savalia, D and Molineux, I. gp3.5muramoyl-L-alanine amidase K1F Scholl, D and Merril, C CKV1F_gp16muramoyl-L-alanine amidase T3 Pajunen, M. I. and Mollineux, I. J. T3p18muramoyl-L-alanine amidase GH-1 Kropinski, A. M. and Kovalyova, I. V.gh-1p12 muramoyl-L-alanine amidase K11 Molineux, I. and Savalia, D.gp3.5 muramoyl-L-alanine amidase ΦCTX Nakayama, K and Hayashi, T. ORF12PG-binding domain (N)/muramidase (C) BCEP43 Summer, E J and Young, R.Bcep43-27 PG-binding domain (N)/muramidase (C) BCEP781 Summer, E J andYoung, R. Bcep781-27 PG-binding domain (N)/muramidase (C) BCEP1 Summer,E J and Young, R. Bcep1-28 PG-binding domain (N)/muramidase (C) BCEPNY3Summer, E J and Young, R. BcepNY3gene26 PG-binding domain (N)/muramidase(C) ΦE12-2 DeShazer, D and Nierman, W. C. gp45 PG-binding domain(N)/muramidase (C) Φ52237 DeShazer, D and Nierman, W. C. gp28 PG-bindingdomain (N)/muramidase (C) ΦP27 Recktenwald, J and Schmidt, H. P27p30endopeptidase RB49 Monod, C and Krisch, H. M. RB49p102 endopeptidase Φ1Arbiol, C. and Comeau, A. M. phi1-p102 endopeptidase T5 Pankova, N. V.and Ksenzenko, V. N. lys (T5.040) endopeptidase 201phi2-1 Thomas et al.,2008 PG-binding domain (N)/unknown catalytic domain (C) Aeh1 Monod, Cand Krisch, H. M. Aeh1p339 muraminidase (T4-like) YYZ-2008 Kropinski, A.M. YYZgp45 muraminidase (lambda-like)

Also preferred is the endolysin part deriving from endolysins of thePseudomonas aeruginosa phages ΦKZ and EL, of the Pseudomonas putidaphage, of the E. coli phage N4, of the phage LUZ24, gp61 muramidase,STM0016 endolysin and PSP3 endolysin.

Further examples for the endolysin part is selected from the groupconsisting of phiKZgp144 according to SEQ ID NO:1, ELgp188 according toSEQ ID NO:2, Salmonella endolysin according to SEQ ID NO:3,Enterobacteria phage T4 endolysin according to SEQ ID NO:4,Acinetobacter baumanii endolysin according to SEQ ID NO:5, E. coli PhageK1F endolysin according to SEQ ID NO:18, OBPgpLYS according to SEQ IDNO:34, PSP3 Salmonella endolysin (PSP3gp10) according to SEQ ID NO:20,E. coli Phage P2 endolysin (P2gp09) according to SEQ ID NO:21,Salmonella typhimurium phage muramidase STM0016 according to SEQ IDNO:22, E. coli Phage N4 muramidase N4-gp61 according to SEQ ID NO:23 andN4-gp61 trunc. according to SEQ ID NO:24, KZ144 according to SEQ IDNO:25.

In another preferred embodiment of the present invention the endolysins,autolysins and bacteriocins of the fusion protein according to thepresent invention comprise modifications and/or alterations of the aminoacid sequences. Such alterations and/or modifications may comprisemutations such as deletions, insertions and additions, substitutions orcombinations thereof and/or chemical changes of the amino acid residues,e.g. biotinylation, acetylation, pegylation, chemical changes of theamino-, SH- or carboxyl-groups. Said endolysins, autolysins andbacteriocins of the fusion protein according to the present inventionexhibit the lytic activity of the respective wild-type endolysin,autolysin and bacteriocins. However, said activity can be the same,higher or lower as the activity of the respective wild-type endolysin.Said activity can be about 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110,120, 130, 140, 150, 160, 170, 180, 190 or about 200% of the activity ofthe respective wild-type endolysin or even more. The activity can bemeasured by assays well known in the art by a person skilled in the artas e.g. the plate lysis assay or the liquid lysis assay which are e.g.described in (Briers et al., J. Biochem. Biophys Methods 70: 531-533,(2007) or Donovan D M, Lardeo M Foster-Frey J. FEMS Microbiol Lett. 2006December; 265(1) or similar publications.

Preferably, the peptide stretch of the fusion protein according to theinvention is fused to the N-terminus and/or to the C-terminus of theendolysin, autolysin or bacteriocin. In a particular preferredembodiment said peptide stretch is only fused to the N-terminus of theenzyme. In another preferred embodiment the peptide stretch is onlyfused to the C-terminus of the enzyme. However, also preferred aremodified fusion proteins having a peptide stretch both on the N-terminusand on the C-terminus. Said peptide stretches on the N-terminus and onthe C-terminus can be the same or distinct peptide stretches. Thepeptide stretch can be linked to the enzyme by additional amino acidresidues e.g. due to cloning reasons. Preferably said peptide stretchcan be linked to the fusion protein by at least 1, 2, 3, 4, 5, 6, 7, 8,9 or 10 additional amino acid residues. In a preferred embodiment thepeptide stretch is linked to the enzyme by the additional amino acidresidues glycine and serine (Gly-Ser) or leucine and glutamic acid(Leu-Glu). Moreover, the peptide stretch of the fusion protein accordingto the invention further comprises additional amino acids on itsN-terminus. Preferably the peptide stretch comprises the amino acidmethionine (Met), alanine and methionine and glycine (Ala-Met-Gly-Ser)or alanine and methionine and glycine and serine (Ala-Met-Gly-Ser).

The peptide stretch of the fusion protein according to the presentinvention is preferably covalently bound to the enzyme. Preferably, saidpeptide stretch consists of at least 5, more preferably at least of 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79,80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97,98, 99 or at least 100 amino acid residues. Especially preferred is apeptide stretch comprising about 5 to about 100 amino acid residues,about 5 to about 50 or about 5 to about 30 amino acid residues. Morepreferred is a peptide stretch comprising about 6 to about 42 amino acidresidues, about 6 to about 39 amino acid residues, about 6 to about 38amino acid residues, about 6 to about 31 amino acid residues, about 6 toabout 25 amino acid residues, about 6 to about 24 amino acid residues,about 6 to about 22 amino acid residues, about 6 to about 21 amino acidresidues, about 6 to about 20 amino acid residues, about 6 to about 19amino acid residues, about 6 to about 16 amino acid residues, about 6 toabout 14 amino acid residues, about 6 to about 12 amino acid residues,about 6 to about 10 amino acid residues or about 6 to about 9 amino acidresidues.

Preferably, the peptide stretch is no tag such as a His-tag, Strep-tag,Avi-tag, Myc-tag, Gst-tag, JS-tag, cystein-tag, FLAG-tag or other tagsknown in the art and no thioredoxin or maltose binding proteins (MBP).However, the peptide stretch and/or the endolysin, autolysin orbacteriocin according to the present invention may comprise in additionsuch tag or tags.

More preferably the peptide stretch has the function to lead the fusionprotein through the outer membrane but may have activity or may have noor only low activity when administered without being fused to theenzyme. The function to lead the fusion protein through the outermembrane of Gram-negative bacteria is caused by the potential of theouter membrane or LPS disrupting or permeabilising or destabilizingactivity of said peptide stretch.

In one aspect of the present invention the fused peptide stretch is anamphipatic peptide, which comprises one or more of the positivelycharged amino acid residues of lysine, arginine and/or histidine,combined to one or more of the hydrophobic amino acid residues ofvaline, isoleucine, leucine, methionine, phenylalanine, tryptophan,cysteine, alanine, tyrosine, histidine, threonin, serine, proline and/orglycine. Side chains of the amino acid residues are preferably orientedin order that cationic and hydrophobic surfaces are clustered atopposite sides of the peptide. Preferably, more than about 30, 40, 50,60 or 70% of the amino acid residues in said peptide are positivelycharged amino acid. Preferably, more than about 30, 40, 50, 60 or 70%,of the amino acid residues in said peptide are hydrophobic amino acidresidues. Advantageously, the amphipathic peptide is fused to theN-terminal and/or the C-terminal end of the enzyme having cell walldegrading activity, thus enhancing the amphipathicity of the latterproteins.

In another embodiment of the invention, the amphipathic peptide fused tothe enzyme consists of at least 5, more preferably at least of 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,45, 46, 47, 48, 49 or 50 amino acid residues. In a preferred embodimentat least about 30, 40, 50, 60 or 70% of the said amino acid residues ofthe amphipatic peptide are either arginine or lysine residues and/or atleast about 30, 40, 50, 60 or 70% of the said amino acid residues of theamphipathic peptide are of the hydrophobic amino acids valine,isoleucine, leucine, methionine, phenylalanine, tryptophan, cysteine,alanine, tyrosine, histidine, threonin, serine, proline and/or glycine.

Preferred amphipatic peptides are Pleurocidin according to SEQ ID NO:6,Cecropin P1 according to SEQ ID NO:7, Buforin II according to SEQ IDNO:8, Buforin I according to SEQ ID NO:19 and Magainin according to SEQID NO:9. Further preferred amphipatic peptides are Cathelidicine e.g.LL-37 according to SEQ ID NO:10, Nigrocine 2 according to SEQ ID NO:26and Ascaphine 5 according to SEQ ID NO:27.

In a further aspect of the present invention the fused peptide stretchis an antimicrobial peptide, which comprises a positive net charge andaround 50% hydrophobic amino acids. The antimicrobial peptides areamphipathic, with a length of about 12 to about 50 amino acid residues.

Specific examples of antimicrobial peptides according to the presentinvention are listed in the following table.

TABLE 2 Peptid Sequenz LL-37 LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTESSEQ ID NO: 10 SMAP-29 RGLRRLGRKIAHGVKKYGPTVLRIIRIAG SEQ ID NO: 11Indolicidin ILPWKWPWWPWRR SEQ ID NO: 12 Protegrin RGGRLCYCRRRFCVCVGRSEQ ID NO: 13 Cecropin P1 SWLSKTAKKLENSAKKRISEGIAIAIQGGPR SEQ ID NO: 7Magainin GIGKFLHSAKKFGKAFVGEIMNS SEQ ID NO: 9 PleurocidinGWGSFFKKAAHVGKHVGKAALTHYL SEQ ID NO: 6 Cecropin AGGLKKLGKKLEGAGKRVFNAAEKALPVVAGAKALRK SEQ ID NO: 14 (A.aegypti)Cecropin A (D. GWLKKIGKKIERVGQHTRDATIQGLGIPQQAANVAATARG SEQ ID NO: 15melanogaster) Buforin II TRSSRAGLQFPVGRVHRLLRK SEQ ID NO: 8Sarcotoxin IA GWLKKIGKKIERVGQHTRDATIQGLGIAQQAANVAATAR SEQ ID NO: 16Apidaecin ANRPVYIPPPRPPHPRL SEQ ID NO: 28 Ascaphine 5GIKDWIKGAAKKLIKTVASHIANQ SEQ ID NO: 27 Nigrocine 2GLLSKVLGVGKKVLCGVSGLVC SEQ ID NO: 26 Pseudin 1 GLNTLKKVFQGLHEAIKLINNHVQSEQ ID NO: 29 Ranalexin FLGGLIVPAMICAVTKKC SEQ ID NO: 30 MelittinGIGAVLKVLTTGLPALISWIKRKRQQ SEQ ID NO: 31

In a further aspect of the present invention the fused peptide stretchis a sushi peptide which is described by Ding J L, Li P, Ho B Cell MolLife Sci. 2008 April; 65(7-8):1202-19. The Sushi peptides: structuralcharacterization and mode of action against Gram-negative bacteria.Especially preferred is the sushi 1 peptide according to SEQ ID NO:32.

Preferred sushi peptides are sushi peptides S1 and S3 and multiplesthereof; FASEB J. 2000 September; 14(12):1801-13.

In a further aspect of the present invention the fused peptide stretchis a defensin, preferably Cathelicidine, Cecropin P1, Cecropin A orMagainin II.

In a further aspect of the present invention the fused peptide stretchis a hydrophobic peptidee.g. Apidaecine having the amino acid sequenceaccording to SEQ ID NO:28, WLBU2-Variant having the amino acid sequenceaccording to SEQ ID NO:33 and Walmaghl having the amino acid sequenceaccording to SEQ ID NO:35. The hydrophobic peptide having the amino acidsequence Phe-Phe-Val-Ala-Pro (SEQ ID NO:17) is not part of the presentinvention.

In another preferred embodiment of the present invention the peptidestretches of the fusion protein according to the present inventioncomprise modifications and/or alterations of the amino acid sequences.Such alterations and/or modifications may comprise mutations such asdeletions, insertions and additions, substitutions or combinationsthereof and/or chemical changes of the amino acid residues, e.g.biotinylation, acetylation, peglyation, chemical changes of the amino-,SH- or carboxyl-groups.

Specific examples of fusion proteins according to the present inventionare listed in the following table:

TABLE 3 Peptide stretch Fusion Fusion (N-terminal unless protein proteinEnzyme part otherwise indicated) P1-E6 SEQ ID NO: 36 KZ144 Ascaphine 5(SEQ ID NO: 25) (SEQ ID NO: 27) P2-E6 SEQ ID NO: 37 KZ144 Apiadaecine(SEQ ID NO: 25) (SEQ ID NO: 28) P3-E6 SEQ ID NO: 38 KZ144 Nigrocine 2(SEQ ID NO: 25) (SEQ ID NO: 26) P4-E6 SEQ ID NO: 39 KZ144 Pseudin 1 (SEQID NO: 25) (SEQ ID NO: 29) P7-E6 SEQ ID NO: 40 KZ144 Ranalexin (SEQ IDNO: 25) (SEQ ID NO: 30) P8-E6 SEQ ID NO: 41 KZ144 WLBU2-Variant (SEQ IDNO: 25) (SEQ ID NO: 33) P9-E6 SEQ ID NO: 42 KZ144 Sushi 1 (SEQ ID NO:25) (SEQ ID NO: 32) P10-E6 SEQ ID NO: 43 KZ144 Melittin (SEQ ID NO: 25)(SEQ ID NO: 31) P11-E6 SEQ ID NO: 44 KZ144 LL-37 (SEQ ID NO: 25) (SEQ IDNO: 10) P12-E6 SEQ ID NO: 45 KZ144 Indolicidin (SEQ ID NO: 25) (SEQ IDNO: 12) P13-E6 SEQ ID NO: 46 KZ144 SMAP-29 (SEQ ID NO: 25) (SEQ ID NO:11) P14-E6 SEQ ID NO: 47 KZ144 Protegrin (SEQ ID NO: 25) (SEQ ID NO: 13)P15-E6 SEQ ID NO: 48 KZ144 Cecropin P1 (SEQ ID NO: 25) (SEQ ID NO: 7)P16-E6 SEQ ID NO: 49 KZ144 Magainin (SEQ ID NO: 25) (SEQ ID NO: 9)P17-E6 SEQ ID NO: 50 KZ144 Pleurocidin (SEQ ID NO: 25) (SEQ ID NO: 6)P18-E6 SEQ ID NO: 51 KZ144 Cecropin A (A. (SEQ ID NO: 25) aegypti) (SEQID NO: 14) P19-E6 SEQ ID NO: 52 KZ144 Cecropin A (A. (SEQ ID NO: 25)melanogaster) (SEQ ID NO: 15) P20-E6 SEQ ID NO: 53 KZ144 Buforin II (SEQID NO: 25) (SEQ ID NO: 8) P21-E6 SEQ ID NO: 54 KZ144 Sarcotoxin IA (SEQID NO: 25) (SEQ ID NO: 16) P1-E3 SEQ ID NO: 55 STM0016 Ascaphine 5 (SEQID NO: 22) (SEQ ID NO: 27) SEQ ID NO: 56 STM0016 Nigrocine 2 (SEQ ID NO:22) (SEQ ID NO: 26) SEQ ID NO: 57 STM0016 SMAP-29 (SEQ ID NO: 22) (SEQID NO: 11) SEQ ID NO: 58 STM0016 Sarcotoxin IA (SEQ ID NO: 22) (SEQ IDNO: 16) P10-E4 SEQ ID NO: 59 N4-gp61 Melittin (SEQ ID NO: 23) (SEQ IDNO: 31) SEQ ID NO: 60 N4-gp61 SMAP-29 (SEQ ID NO: 23) (SEQ ID NO: 11)P10-E5 SEQ ID NO: 61 N4-gp61 trunc. Melittin (SEQ ID NO: 24) (SEQ ID NO:31) SEQ ID NO: 62 N4-gp61 trunc. Cecropin P1 (SEQ ID NO: 24) (SEQ ID NO:7) SEQ ID NO: 63 N4-gp61 trunc. SMAP-29 (SEQ ID NO: 24) (SEQ ID NO: 11)

The fusion protein according to the present invention, and thus inparticular the especially preferred fusion proteins according to SEQ IDNO: 36 to 63, may additional comprise a methionine on the N-terminus.

The fusion protein according to the present invention, and thus inparticular the especially preferred fusion proteins according to SEQ IDNO: 36 to 63 may additional comprise a tag e.g. for purification.Preferred is a His6-tag, preferably at the C-terminus and/or theN-terminus of the fusion protein. Said tag can be linked to the fusionprotein by additional amino acid residues e.g. due to cloning reasons.Preferably said tag can be linked to the fusion protein by at least 1,2, 3, 4, 5, 6, 7, 8, 9 or 10 additional amino acid residues. In apreferred embodiment the fusion protein comprises a His6-tag at itsC-terminus linked to the fusion protein by the additional amino acidresidues lysine and glycine (Lys-Gly) or leucine and glutamic acid(Leu-Glu). In another preferred embodiment the fusion protein comprisesa His6-tag at its N-terminus linked to the fusion protein by theadditional amino acid residues lysine and glycine (Lys-Gly) or leucineand glutamic acid (Leu-Glu). In another preferred embodiment the fusionprotein comprises a His6-tag at its N- and C-terminus linked to thefusion protein by the additional amino acid residues lysine and glycine(Lys-Gly) or leucine and glutamic acid (Leu-Glu).

In a more preferred embodiment the fusion protein comprises a His6-tagat its C-terminus linked to the fusion protein by the additional aminoacid residues leucine and glutamic acid (Leu-Glu) and the peptidestretch of the fusion protein according to the invention is linked tothe N-terminus of the enzyme by the additional amino acid residuesglycine and serine. In another preferred embodiment the fusion proteincomprises a His6-tag at its C-terminus linked to the fusion protein bythe additional amino acid residues leucine and glutamic acid (Leu-Glu)and the peptide stretch of the fusion protein according to the inventionis linked to the N-terminus of the enzyme by the additional amino acidresidues glycine and serine (Gly-Ser) and the fusion protein compriseson the N-terminus the additional amino acid residues methionine (Met) oralanine, methionine and glycine (Ala-Met-Gly) or alanine, methionine,glycine and serine (Ala-Met-Gly-Ser). Preferably the fusion proteins areaccording to SEQ ID NO: 77 to 90.

Fusion proteins are constructed by linking at least two nucleic acidsequences using standard cloning techniques as described e.g. bySambrook et al. 2001, Molecular Cloning: A Laboratory Manual. Such aprotein may be produced, e.g., in recombinant DNA expression systems.Such fusion proteins according to the present invention can be obtainedby fusing the nucleic acids for endolysin and the respective peptidestretch.

The fusion proteins according to the present invention may be fused orlinked to other additional proteins. Example for this other additionalprotein is thioredoxin.

The present invention further relates to an isolated nucleic acidmolecule encoding the fusion protein according to the present invention.The present invention further relates to a vector comprising the nucleicacid molecule according to the present invention. Said vector mayprovide for the constitutive or inducible expression of said fusionprotein according to the present invention.

The invention also relates to a method for obtaining said fusionproteins from a micro-organism, such as a genetically modified suitablehost cell which expresses said fusion proteins. Said host cell may be amicro-organism such as bacteria or yeast or an animal cell as e.g. amammalian cell, in particular a human cell. In one embodiment of thepresent invention the host cell is a Pichia pastoris cell. The host maybe selected due to mere biotechnological reasons, e.g. yield,solubility, costs, etc. but may be also selected from a medical point ofview, e.g. a non-pathological bacteria or yeast, human cells.

Another aspect of the present invention is related to a method forgenetically transforming a suitable host cell in order to obtain theexpression of the fusion proteins according to the invention wherein thehost cell is genetically modified by the introduction of a geneticmaterial encoding said fusion proteins into the host cell and obtaintheir translation and expression by genetic engineering methods wellknown by the man skilled in the art.

In a further aspect the present invention relates to a composition,preferably a pharmaceutical composition, comprising a fusion proteinaccording to the present invention and/or a host transformed with anucleic acid molecule or a vector comprising a nucleotide sequenceencoding a fusion protein according to the present invention.

In a preferred embodiment of the present invention the compositioncomprises additionally agents permeabilizing the outer membrane ofGram-negative bacteria such metal chelators as e.g. EDTA, TRIS, lacticacid, lactoferrin, polymyxin, citric acid and/or other substances asdescribed e.g. by Vaara (Agents that increase the permeability of theouter membrane. Vaara M. Microbiol. Rev. 1992 September; 56(3):395-441). Also preferred are compositions comprising combinations ofthe above mentioned permeabilizing agents. Especially preferred is acomposition comprising about 10 μM to about 100 mM EDTA, more preferablyabout 50 μM to about 10 mM EDTA, more preferably about 0.5 mM to about10 mM EDTA, more preferably about 0.5 mM to about 2 mM EDTA, morepreferably about 0.5 mM to 1 mM EDTA. However, also compositionscomprising about 10 μM to about 0.5 mM EDTA are preferred. Alsopreferred is a composition comprising about 0.5 mM to about 2 mM EDTA,more preferably about 1 mM EDTA and additionally about 10 to about 100mM TRIS.

The present invention also relates to a fusion protein according to thepresent invention and/or a host transformed with a nucleic acidcomprising a nucleotide sequence encoding a fusion protein according tothe present invention for use as a medicament. In a further aspect thepresent invention relates to the use of a fusion protein according tothe present invention and/or a host transformed with a vector comprisinga nucleic acid molecule comprising a nucleotide sequence encoding amodified, fusion protein according to the present invention in themanufacture of a medicament for the treatment and/or prevention of adisorder, disease or condition associated with Gram-negative bacteria.In particular the treatment and/or prevention of the disorder, diseaseor condition may be caused by Gram-negative bacteria of bacterialgroups, families, genera or species comprising strains pathogenic forhumans or animals like Enterobacteriaceae (Escherichia, especially E.coli, Salmonella, Shigella, Citrobacter, Edwardsiella, Enterobacter,Hafnia, Klebsiella, especially K. pneumoniae, Morganella, Proteus,Providencia, Serratia, Yersinia), Pseudomonadaceae (Pseudomonas,especially P. aeruginosa, Burkholderia, Stenotrophomonas, Shewanella,Sphingomonas, Comamonas), Neisseria, Moraxella, Vibrio, Aeromonas,Brucella, Francisella, Bordetella, Legionella, Bartonella, Coxiella,Haemophilus, Pasteurella, Mannheimia, Actinobacillus, Gardnerella,Spirochaetaceae (Treponema and Borrelia), Leptospiraceae, Campylobacter,Helicobacter, Spirillum, Streptobacillus, Bacteroidaceae (Bacteroides,Fusobacterium, Prevotella, Porphyromonas), Acinetobacter, especially A.baumanii.

The present invention further relates to a medicament comprising afusion protein according to the present invention and/or a hosttransformed with a nucleic acid comprising a nucleotide sequenceencoding a fusion protein according to the present invention.

In a further aspect the present invention relates to a method oftreating a disorder, disease or condition in a subject in need oftreatment and/or prevention, which method comprises administering tosaid subject an effective amount of a fusion protein according to thepresent invention and/or an effective amount of a host transformed witha nucleic acid comprising a nucleotide sequence encoding a fusionprotein according to the present invention or a composition according tothe present invention. The subject may be a human or an animal.

In particular said method of treatment may be for the treatment and/orprevention of infections of the skin, of soft tissues, the respiratorysystem, the lung, the digestive tract, the eye, the ear, the teeth, thenasopharynx, the mouth, the bones, the vagina, of wounds of bacteraemiaand/or endocarditis caused by Gram-negative bacteria, in particular bythe Gram-negative bacteria as listed above.

The dosage and route of administration used in a method of treatment (orprophylaxis) according to the present invention depends on the specificdisease/site of infection to be treated. The route of administration maybe for example oral, topical, nasopharyngeal, parenteral, intravenous,rectal or any other route of administration.

For application of a fusion protein according to the present inventionand/or an effective amount of a host transformed with a nucleic acidcomprising a nucleotide sequence encoding a fusion protein according tothe present invention or a composition according to the presentinvention to a site of infection (or site endangered to be infected) aformulation may be used that protects the active compounds fromenvironmental influences such as proteases, oxidation, immune responseetc., until it reaches the site of infection. Therefore, the formulationmay be capsule, dragee, pill, powder, suppository, emulsion, suspension,gel, lotion, cream, salve, injectable solution, syrup, spray, inhalantor any other medical reasonable galenic formulation. Preferably, thegalenic formulation may comprise suitable carriers, stabilizers,flavourings, buffers or other suitable reagents. For example, fortopical application the formulation may be a lotion, cream, gel, salveor plaster, for nasopharyngeal application the formulation may be salinesolution to be applied via a spray to the nose. For oral administrationin case of the treatment and/or prevention of a specific infection sitee.g. in the intestine, it can be necessary to protect a fusion proteinaccording to the present invention from the harsh digestive environmentof the gastrointestinal tract until the site of infection is reached.Thus, bacteria as carrier, which survive the initial steps of digestionin the stomach and which secret later on a fusion protein according tothe present invention into the intestinal environment can be used.

In a specific embodiment of the present invention the use of a fusionprotein according to the present invention and/or a host transformedwith a vector comprising a nucleic acid molecule comprising a nucleotidesequence encoding a fusion protein according to the present invention inthe manufacture of a medicament for the treatment and/or prevention of adisorder, disease or condition caused by Pseudomonas, particularly byPseudomonas aeruginosa in particular intestinal affections, inparticular in infants, infections of the meninges, e.g. meningitishaemorrhagica, infections of the middle ear, the skin (Ecthymagangraenosum), in particular burns, the urinary tract, rhinitis,bacteremic pneumonia, in particular wherein the patient is sufferingfrom cystic fibrosis or hematologic malignancies such as leukemia, orwith neutropenia from immunosuppressive therapy, septicemia, inparticular because of long-term intravenous or urinary catheterization,invasive surgical procedures and severe burns, endocarditis, inparticular wherein the patient is a intravenous drug user or a patientwith complications from open heart surgery, highly destructive ocularinfections, in particular after the use of contaminated ophthalmologicsolutions or severe facial burns, osteochondritis, in particular as aresult of severe trauma or puncture wounds through contaminatedclothing.

In another specific embodiment of the present invention the disorder,disease or condition is caused by Burkholderia pseudomallei, inparticular Whitmore's Disease, chronic pneumonia, septicemia, inparticular wherein the patient has a traumatized skin lesion.

In another specific embodiment of the present invention the disorder,disease or condition is caused by Salmonella thyphimurium and Salmonellaenteritidis, in particular acute gastroenteritis and local purulentprocesses, particularly osteomyelitis, endocarditis, cholecystitis andespecially caused by Salmonella thyphimurium meningitis, in particularwherein the patient is less than two years old.

In another specific embodiment of the present invention the disorder,disease or condition is caused by Salmonella typhi, in particular typus.

In another specific embodiment of the present invention the disorder,disease or condition is caused by Salmonell paratyphi, in particularparatyphus.

In another specific embodiment of the present invention the disorder,disease or condition is caused by Acinetobacter baumannii, in particularbronchitis, pneumonia, wound infections and septicemia, in particular asa result of intravenous catheterization.

In another specific embodiment of the present invention the disorder,disease or condition is caused by Escherichia coli, in particular extraintestinal infections, particularly appendicitis, purulentcholecystitis, peritonitis, purulent meningitis and infection of theurinary tract, intraintestinal E. coli infections, particularly epidemicenteritis, and infectious disease similar to dysentery, septicemia,enterotoxemia, mastitis and dysentery.

In another specific embodiment of the present invention the disorder,disease or condition is caused by Klebsiella pneumoniae, in particularpneumonia, bacteremia, meningitis and infections of the urinary tract.

Preferably, a fusion protein according to the present invention is usedfor medical treatment, if the infection to be treated (or prevented) iscaused by multiresistant bacterial strains, in particular by strainsresistant against one or more of the following antibiotics:streptomycin, tetracycline, cephalothin, gentamicin, cefotaxime,cephalosporin, ceftazidime or imipenem. Furthermore, a fusion proteinaccording to the present invention can be used in methods of treatmentby administering it in combination with conventional antibacterialagents, such as antibiotics, lantibiotics, bacteriocins or endolysins,etc.

The present invention also relates to a pharmaceutical pack comprisingone or more compartments, wherein at least one compartment comprises oneor more fusion protein according to the present invention and/or one ormore hosts transformed with a nucleic acid comprising a nucleotidesequence encoding a fusion protein according to the present invention ora composition according to the present invention,

In another aspect the present invention relates to a process ofpreparation of a pharmaceutical composition, said process comprisingadmixing one or more fusion protein according to the present inventionand/or one or more hosts transformed with a nucleic acid comprising anucleotide sequence encoding a fusion protein according to the presentinvention with a pharmaceutically acceptable diluent, excipient orcarrier.

In an even further aspect the composition according to the presentinvention is a cosmetic composition. Several bacterial species can causeirritations on environmentally exposed surfaces of the patient's bodysuch as the skin. In order to prevent such irritations or in order toeliminate minor manifestations of said bacterial pathogens, specialcosmetic preparations may be employed, which comprise sufficient amountsof the fusion protein according to the present invention in order todegrade already existing or freshly settling pathogenic Gram-negativebacteria.

In a further aspect the present invention relates to the fusion proteinaccording to the present invention for use as diagnostic means inmedicinal, food or feed or environmental diagnostics, in particular as adiagnostic means for the diagnostic of bacteria infection caused inparticular by Gram-negative bacteria. In this respect the fusion proteinaccording to the present invention may be used as a tool to specificallydegrade pathogenic bacteria, in particular Gram-negative pathogenicbacteria. The degradation of the bacterial cells by the fusion proteinaccording to the present invention can be supported by the addition ofdetergents like Triton X-100 or other additives which weaken thebacterial cell envelope like polymyxin B. Specific cell degradation isneeded as an initial step for subsequent specific detection of bacteriausing nucleic acid based methods like PCR, nucleic acid hybridization orNASBA (Nucleic Acid Sequence Based Amplification), immunological methodslike IMS, immunofluorescence or ELISA techniques, or other methodsrelying on the cellular content of the bacterial cells like enzymaticassays using proteins specific for distinct bacterial groups or species(e.g. β-galactosidase for enterobacteria, coagulase for coagulasepositive strains).

In a further aspect the present invention relates to the use of thefusion protein according to the present invention for the treatment,removal, reduction or prevention of Gram-negative bacterialcontamination of foodstuff, of food processing equipment, of foodprocessing plants, of surfaces coming into contact with foodstuff suchas shelves and food deposit areas and in all other situations, wherepathogenic, facultative pathogenic or other undesirable bacteria canpotentially infest food material, of medical devices and of all kind ofsurfaces in hospitals and surgeries.

In particular, a fusion protein of the present invention may be usedprophylactically as sanitizing agent. Said sanitizing agent may be usedbefore or after surgery, or for example during hemodialysis. Moreover,premature infants and immunocompromised persons, or those subjects withneed for prosthetic devices may be treated with a fusion proteinaccording to the present invention. Said treatment may be eitherprophylactically or during acute infection. In the same context,nosocomial infections, especially by antibiotic resistant strains likePseudomonas aeruginosa (FQRP), Acinetobacter species andEnterobacteriaceae such as E. coli, Salmonella, Shigella, Citrobacter,Edwardsiella, Enterobacter, Hafnia, Klebsiella, Morganella, Proteus,Providencia, Serratia and Yersinia species may be treatedprophylactically or during acute phase with a fusion protein of thepresent invention. Therefore, a fusion protein according to the presentinvention may be used as a disinfectant also in combination with otheringredients useful in a disinfecting solution like detergents, tensids,solvents, antibiotics, lanthibiotics, or bacteriocins.

For the use of the fusion protein according to the present invention asa disinfectant e.g. in hospital, dental surgery, veterinary, kitchen orbathroom, the fusion protein can be prepared in a composition in form ofe.g. a fluid, a powder, a gel, or an ingredient of a wet wipe or adisinfection sheet product. Said composition may additionally comprisesuitable carrier, additives, diluting agents and/or excipients for itsrespective use and form, respectively, —but also agents that support theantimicrobial activity like EDTA or agents enhance the antimicrobialactivity of the fusion proteins. The fusion protein may also be usedwith common disinfectant agents like, Alcohols, Aldehydes, Oxidizingagents, Phenolics, Quaternary ammonium compounds or UV-light. Fordisinfecting for example surfaces, objects and/or devices the fusionprotein can be applied on said surfaces, objects and/or devices. Theapplication may occur for instance by wetting the disinfectingcomposition with any means such as a cloth or rag, by spraying, pouring.The fusion proteins may be used in varying concentration depending onthe respective application and the “reaction time” intended to obtainfull antimicrobial activity.

Another aspect of the present invention is that the invention can beused like a tool box, i.e. any peptide stretch disclosed above may befused to any endolysin, autolysin or bacteriocin disclosed herein. Thus,it is possible to combine the respective peptide stretch, which enablesthe binding of the fusion protein to the respective bacteria and theendolysin, autolysin or bacteriocin, which inhibit the growth of therespective bacteria. Consequently, it is possible to construct asuitable fusion protein for any bacteria which should be eliminated.

Further scope of applicability of the present invention will becomeapparent from the detailed description given hereinafter, however, itshould be understood that the detailed description and specificexamples, while indicating preferred embodiments of the invention, aregiven by way of illustration only, since various changes andmodifications within the spirit and scope of the invention will becomeapparent to those skilled in the art from this detailed description. Itis to be understood that both the foregoing general description and thefollowing detailed description are exemplary and explanatory only andare not restrictive of the invention, as claimed.

The following examples explain the present invention but are notconsidered to be limiting. Unless indicated differently, molecularbiological standard methods were used, as e.g., described by Sambrock etal., 1989, Molecular Cloning: A Laboratory Manual, 2nd edition, ColdSpring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

EXAMPLE 1. CLONING, EXPRESSION AND PURIFICATION OF GP144 AND GP188MODIFIED WITH AN AMPHIPATHIC PEPTIDE

As a proof of principle, the potential of the LPS disrupting activity ofamphipathic peptides to lead gp144 and gp188 through the outer membraneand the consequent antibacterial activity against Gram-negative bacteriais demonstrated. Gp144 and gp188 are modular endolysins originating fromPseudomonas aeruginosa phages φKZ and EL with an N-terminalpeptidoglycan binding and C-terminal catalytic domain (Briers et al.,2007).

To extend the 5′ end of the open reading frame encoding gp144 or gp188with a gene fragment encoding the amphipathic α4 helix of T4 lysozyme(aa 143-155: Pro-Asn-Arg-Ala-Lys-Arg-Val-Ile-Thr-Thr-Phe-Arg-Thraccording to SEQ ID NO: 92) a tail PCR with an extended 5′ primer andstandard 3′ primer was applied. The PCR product was cloned in thepEXP5CT/TOPO® expression vector (Invitrogen, Carlsbad, Calif., USA).

Expression of all constructs was performed in E. coli BL21 (DE3) pLysScells. All proteins were purified by Ni²⁺ affinity chromatography usingthe C-terminal 6×His-tag. The yields for different purifications areshown in table 4. Remarkably, α4-KZ144 production was not toxic for thehost, in contrast to KZ144, resulting in a significant higher yield.

Purified stock solutions were ˜90% pure. All gp144 derivatives showedmultimer formation which could be converted to monomers by addition ofβ-mercapto-ethanol, indicating that interdisulfide bonds causemultimerization.

TABLE 4 Yields of recombinant purification of endolysins modified withan amphipathic peptide*. Endolysin Fusion gp144 gp188 α4 helix 179 mg 38mg *The total yield of purified recombinant protein per liter E. coltexpression culture is shown. This value was determined byspectrophotometric measurement of the protein concentration and thetotal volume of the purified stock solution. The purification of gp188derivatives was performed under more stringent conditions (65 mMimidazole) compared to gp144 derivatives (50 mM imidazole) to ensurehigh purity.Characterization of Gp144 and Gp188 Modified with an Amphipathic Peptide1.A. Enzymatic Activity of Gp144 and Gp188 Modified with an AmphipathicPeptide

To assess the influence of the modification on the enzymatic activity ofgp144 or gp188, the specific activity of the variants was measured onchloroform-permeabilized Pseudomonas aeruginosa cells and compared tothe corresponding unmodified endolysin. Different incremental amounts ofall modified endolysins were tested to determine the correspondingsaturation curve.

The slope of the linear regression of the linear region of this curve isa measure for the specific activity and was expressed relatively to theslope of unmodified gp144 or gp188 (Table 5).

TABLE 5 Enzymatic activity of gp144 or gp188 modified with anamphipathic peptide*. Endolysin Fusion gp144 gp188 α4 helix 23% 146%*The specific enzymatic activity of the different variants wasdetermined and expressed relatively to the specific activity of thecorresponding original endolysin (=100%), which was testedsimultaneously. The buffer conditions of the assay were the optimalconditions of the corresponding endolysins (KH₂P0₄/K₂HP0₄ I = 120 mM pH6.2 and I = 80 mM pH 7.3 for gp144 and gp188, respectively).1.B. Antibacterial Activity of Gp144 and Gp188 Modified with anAmphipathic Peptide

Exponential (˜10⁶/ml) P. aeruginosa PAO1 cells were incubated at roomtemperature with unmodified and modified gp144/gp188. After 1 hour, cellsuspensions were diluted and plated. The residual colonies were countedafter an overnight incubation (Table 6). Unmodified gp144 gp188 does notreduce cell numbers significantly compared to the negative control. Thisobservation illustrates the efficacy of the outer membrane as a barrier.Fusion proteins with the amphipathic α4-helix inactivate exponentialcells with 50±11 and 34±11% for α4-KZ144 and α4-EL188, respectively.When stationary cells with a 100-fold higher density are used, thesevalues are similar (35±18 and 32±17%, respectively). Despite the ratherhigh variability between different replicates, these values differsignificantly from the untreated cells (α=0.05). In general, modifiedgp144 derivatives tend to have a higher antibacterial activity thangp188 derivatives.

TABLE 6 Antibacterial effect of endolysins gp144 and gp188 and theirderivatives*. Exponentially Endolysins growing cells gp144 gp188 Fusion% log % log unmodified  0 ± 15 0.00 ± 0.06 10 ± 13 0.05 ± 0.06 α4 helix50 ± 11 0.31 ± 0.09 34 ± 11 0.19 ± 0.07 *Exponentially growing P.aeruginosa PAO1 cells were 100 x diluted and incubated (final densitywas ~10⁶/ml) with 10 μg undialyzed protein (final concentration 100μg/ml, buffer: 20 mM NaH₂P0₄—NaOH pH 7.4; 0.5M NaCl; 0.5M imidazole) for1 hour at room temperature. Aliquots are diluted and plated. Theantibacterial activity is expressed as the relative inactivation (%)(=100 − (N_(i)/No)*100 with N₀ = number of untreated cells and N_(i) =number of treated cells) and in logarithmic units (=log₁₀N₀/N_(i)). Allsamples were replicated in six fold. Averages/standard deviations arerepresented. Statistical analysis was performed using a student'st-test.

EXAMPLE 2. CLONING, EXPRESSION AND PURIFICATION OF GP144 AND GP188MODIFIED WITH A HYDROPHOBIC PEPTIDE

As a proof of principle, the potential of the LPS disrupting activity ofa hydrophobic pentapeptides to lead gp144 and gp188 through the outermembrane and the consequent antibacterial activity against Gram-negativebacteria is demonstrated. Gp144 and gp188 are modular endolysinsoriginating from Pseudomonas aeruginosa phages φKZ and EL with anN-terminal peptidoglycan binding and C-terminal catalytic domain (Brierset al., 2007).

To extend the 5′ end of the open reading frame encoding gp144 or gp188with a gene fragment encoding 5 hydrophobic residues(Phe-Phe-Val-Ala-Pro) a tail PCR with an extended 5′ primer and standard3′ primer was applied. The PCR product was cloned in the pEXP5CT/TOPO®expression vector (Invitrogen, Carlsbad, Calif., USA).

Expression of all constructs was performed in E. coli BL21 (DE3) pLysScells. All proteins were purified by Ni2+ affinity chromatography usingthe C-terminal 6×His-tag. The yields for different purifications areshown in table 7.

Purified stock solutions were ˜90% pure. All gp144 derivatives showedmultimer formation which could be converted to monomers by addition ofβ-mercapto-ethanol, indicating that interdisulfide bonds causemultimerization.

TABLE 7 Yields of recombinant purification of endolysin derivatives*.Endolysin Fusion gp144 gp188 Phe-Phe-Val-Ala-Pro 25 mg 85 mg *The totalyield of purified recombinant protein per liter E. colt expressionculture is shown. This value was determined by spectrophotometricmeasurement of the protein concentration and the total volume of thepurified stock solution. The purification of gp188 derivatives wasperformed under more stringent conditions (65 mM imidazole) compared togp144 derivatives (50 mM imidazole) to ensure high purity.Characterization of Gp144 and Gp188 Modified with a HydrophobicPentapeptide2.A. Enzymatic Activity of Gp144 and Gp188 Modified with a HydrophobicPentapeptide

To assess the influence of the modifications on the enzymatic activityof gp144 or gp188, the specific activity of the variants was measured onchloroform-permeabilized Pseudomonas aeruginosa cells and compared tothe corresponding unmodified endolysin. Different incremental amounts ofall modified endolysins were tested to determine the correspondingsaturation curve. The slope of the linear regression of the linearregion of this curve is a measure for the specific activity and wasexpressed relatively to the slope of unmodified gp144 or gp188 (Table8).

TABLE 8 Enzymatic activity of gp144 or gp188 modified with a hydrophobicpeptide*. Endolysin Fusion gp144 gp188 Hydrophobic pentapeptide 150%100% *The specific enzymatic activity of the different variants wasdetermined and expressed relatively to the specific activity of thecorresponding original endolysin (=100%), which was testedsimultaneously. The buffer conditions of the assay were the optimalconditions of the corresponding endolysins (KH₂P0₄/K₂HP0₄ I = 120 mM pH6.2 and I = 80 mM pH 7.3 for gp144 and gp188, respectively).2.B. Antibacterial Activity of Gp144 and Gp188 Modified with aHydrophobic Pentapeptide

Exponential (˜10⁶/m1) P. aeruginosa PAO1 cells were incubated at roomtemperature with unmodified and modified gp144/gp188. After 1 hour, cellsuspensions were diluted and plated. The residual colonies were countedafter an overnight incubation (Table 9). Unmodified gp144 gp188 does notreduce cell numbers significantly compared to the negative control. Thisobservation illustrates the efficacy of the outer membrane as a barrier.Incubation with the hydrophobic pentapeptide fusion proteins causes asignificant reduction (α=0.05) of the bacterial cell number (83±7 and69±21% for modified gp144 and gp188, respectively). In general, modifiedgp144 derivatives tend to have a higher antibacterial activity thangp188 derivatives.

TABLE 9 Antibacterial effect of endolysins gp144 and gp188 and theirderivatives*. Exponentially Endolysins growing cells gp144 gp188 Fusion% log % log unmodified  0 ± 15 0.00 ± 0.06 10 ± 13 0.05 ± 0.06Hydrophobic 83 ± 7 0.9 ± 0.2 69 ± 21 0.7 ± 0.3 pentapeptide*Exponentially growing P. aeruginosa PAO1 cells were 100 x diluted andincubated (final density was ~10⁶/ml) with 10 μg undialyzed protein(final concentration 100 μg/ml, buffer: 20 mM NaH₂P0₄—NaOH pH 7.4; 0.5MNaCl; 0.5M imidazole) for 1 hour at room temperature. Aliquots arediluted and plated. The antibacterial activity is expressed as therelative inactivation (%) (=100 − (N_(i)/No)*100 with N₀ = number ofuntreated cells and N_(i) = number of treated cells) and in logarithmicunits (=log₁₀N₀/N_(i)). All samples were replicated in six fold.Averages/standard deviations are represented. Statistical analysis wasperformed using a student's t-test.

EXAMPLE 3: CLONING, EXPRESSION AND PURIFICATION OF KZ144 AND STM0016MODIFIED WITH VARIOUS PEPTIDE STRETCHES ON THE N-TERMINUS OF THEENDOLYSIN

KZ144 according to SEQ ID NO: 25 is a modular endolysin originating fromPseudomonas aeruginosa phage φKZ with an N-terminal peptidoglycanbinding and C-terminal catalytic domain (Briers et al., 2007). Theendolysin KZ144 is encoded by the nucleic acid molecule according to SEQID NO: 64. The nucleic acid molecule according to SEQ ID NO: 64 wassynthetically produced with a BamH I (5″-GGA TCC-3′) restriction site atthe 5″-end of the nucleic acid molecule and an Xho I (5′-CTC GAG-3′)restriction site at the 3′-end of the nucleic acid molecule.

STM0016 is a hypothetical protein with homology to the E. coli phage N4endolysin N4-gp61.

The endolysin STM0016 is encoded by the nucleic acid molecule accordingto SEQ ID NO: 65. The nucleic acid molecule according to SEQ ID NO: 65was synthetically produced with a BamH I (5′-GGA TCC-3′) restrictionsite at the 5′-end of the nucleic acid molecule and an Xho I (5″-CTCGAG-3′) restriction site at the 3′-end of the nucleic acid molecule.

N4-gp61 is an E. coli N4 phage endolysin. The endolysin is encoded bythe nucleic acid according to SEQ ID NO: 91. The nucleic acid moleculeaccording to SEQ ID NO: 91 was synthetically produced with a BamH I(5″-GGA TCC-3′) restriction site at the 5″-end of the nucleic acidmolecule and an Xho I (5′-CTC GAG-3′) restriction site at the 3′-end ofthe nucleic acid molecule.

The following peptide stretches in table 10 were used for production offusion proteins with the endolysin KZ144 or STM0016:

TABLE 10 Nucleic acid molecule encoding Peptide stretch the peptidestretch Pseudin 1 SEQ ID NO: 66 (SEQ ID NO: 29) Ranalexin SEQ ID NO: 67(SEQ ID NO: 30) Sushi 1 SEQ ID NO: 68 (SEQ ID NO: 32) WLBU2-Variant SEQID NO: 69 (SEQ ID NO: 33) Melittin SEQ ID NO: 70 (SEQ ID NO: 31) SMAP-29SEQ ID NO: 71 (SEQ ID NO: 11) Pleurocidin SEQ ID NO: 72 (SEQ ID NO: 6)Cecropin A (A. SEQ ID NO: 73 aegypti) (SEQ ID NO: 14) Cecropin A (A. SEQID NO: 74 melanogaster) (SEQ ID NO: 15) Buforin II SEQ ID NO: 75 (SEQ IDNO: 8) Sarcotoxin IA SEQ ID NO: 76 (SEQ ID NO: 16)

The nucleic acid molecules encoding the respective peptide stretcheswere synthetically produced with a Nde I (5′-CAT ATG-3′) restrictionsite at the 5′-end of the nucleic acid molecule and a BamH I (5′-GGATCC-3′) restriction site at the 3′-end of the nucleic acid molecule,except the nucleic acid molecule encoding the Sushi 1 peptide, which wasproduced with a Nco I restriction site plus two additional nucleotides(5′-CCA TGG GC-3′) at the 5′-end of the nucleic acid molecule.

Fusion proteins are constructed by linking at least two nucleic acidsequences using standard cloning techniques as described e.g. bySambrook et al. 2001, Molecular Cloning: A Laboratory Manual. Thereforethe nucleic acid molecules encoding the peptide stretches were cleavedin a digest with the respective restriction enzymes Nde I and BamH I andin case of the nucleic acid molecule encoding the peptide stretch Sushi1 the digest was performed with the restriction enzymes Nco I and BamHI. Subsequently the cleaved nucleic acids encoding the peptide stretcheswere ligated into the pET21 b expression vector (Novagen, Darmstadt,Germany), which was also cleaved in a digest with the respectiverestriction enzymes Nde land BamH I before. The cleaved nucleic acidmolecule encoding the peptide stretch Sushi I was ligated into amodified pET32 b expression vector (unmodified vector obtainable fromNovagen, Darmstadt, Germany), which was also cleaved in a digest withthe respective restriction enzymes Nco I and BamH I before. Themodification of the pET32b expression vector refers to the deletion ofthe sequence encoding a S-tag and the central His-tag.

Afterwards, the nucleic acid molecule encoding the endolysin KZ144 wascleaved in a digest with the restriction enzyme BamH I and Xho I, sothat the endolysin could be ligated into the pET21b expression vector(Novagen, Darmstadt, Germany) and the modified pET32 b expressionvector, respectively, which were also cleaved in a digest with therespective restriction enzymes BamH I and Xho I before. The nucleic acidmolecule encoding the endolysin STM0016 and the nucleic acid moleculeencoding the endolysin N4gp61 were cleaved in a digest with therestriction enzyme BamH I and Xho I, so that the respective endolysincould be ligated into the pET21b expression vector (Novagen, Darmstadt,Germany).

Thus, the nucleic acid molecule encoding the peptide stretch is ligatedinto the respective vector at the 5′-end of the nucleic acid moleculeencoding the endolysin KZ144 or STM0016. Moreover, the nucleic acidmolecule encoding the endolysin KZ144 or STM0016 is ligated into therespective plasmid, so that a nucleic acid molecule encoding a His-tagconsisting of six histidine residues is associated at the 3′-end of thenucleic acid molecule encoding the endolysin.

As some fusion proteins may either be toxic upon expression in bacteria,or not homogenous due to protein degradation, the strategy might be toexpress these fusion proteins fused or linked to other additionalproteins. Example for these other additional protein is thioredoxin,which was shown to mediate expression of toxic antimicrobial peptides inE. coli (TrxA mediating fusion expression of antimicrobial peptide CM4from multiple joined genes in Escherichia coli. Zhou L, Zhao Z, Li B,Cai Y, Zhang S. Protein Expr Purif. 2009 April; 64(2):225-230). In thecase of the fusion protein consisting of the N-terminal Sushi 1 peptideand the endolysin KZ144, the Sushi 1 peptide is ligated into themodified pET32 b expression vector, so that an additional thioredoxin isassociated at the 5′-end of the Sushi 1 peptide. The thioredoxin couldbe removed from the expressed fusion protein by the use of enterokinase,therefore between the nucleic acid molecule encoding the Sushi peptideand the one encoding the thioredoxin is an enterokinase restriction siteintroduced.

The sequence of the endolysin-peptide-fusions was controlled viaDNA-sequencing and correct clones were transformed into E. coliBL21(DE3) (Novagen, Darmstadt, Germany) for protein expression.

Recombinant expression of the fusion proteins according to SEQ ID NO: 77to 90 is performed in E. coli BL21 (DE3) pLysS and E. coli BL21 (DE3)cells (Novagen, Darmstadt, Germany). The cells were growing until anoptical density of OD600 nm of 0.5-0.8 was reached. Then the expressionof the fusion protein was induced with 1 mM IPTG(isopropylthiogalactoside) and the expression was performed at 37° C.for a period of 4 hours.

E. coli BL21 cells were harvested by centrifugation for 20 min at 6000 gand disrupted via sonication on ice. Soluble and insoluble fraction ofthe E. coli crude extract were separated by centrifugation (Sorvall,SS34, 30 min, 15 000 rpm). All proteins were purified by Ni²⁺ affinitychromatography (Akta FPLC, GE Healthcare) using the C-terminal6×His-tag, encoded by the pET21b or pET32b vectors.

As described above, some of the fusion proteins were expressed using amodified pET32b vector (S-tag and central His-tag deleted), which fusesthioredoxin on the N-terminus of the proteins of interest. The vectoralso contains an enterokinase cleavage site right before the protein ofinterest. This site allows the proteolytic cleavage between thioredoxinand the protein of interest, which can purified via the remainingC-terminal His-tag. For antimicrobial function of the fusion proteinSushi 1-KZ144 it may be necessary to remove the thioredoxin byproteolytic cleavage. Therefore the fusion protein was cleaved with 2-4units/mg recombinant enterokinase (Novagen, Darmstadt, Germany) toremove the thioredoxin following the protocol provided by themanufacturer. After enterokinase cleavage the fusion protein waspurified via His-tag purification as described below.

The Ni²⁺ affinity chromatography is performed in 4 subsequent steps, allat room temperature:

-   -   1. Equilibration of the Histrap FF 5 ml column (GE Healthcare)        with up to 10 column volumes of Washing Buffer (20 mM imidazole,        1 M NaCl and 20 mM Hepes on pH 7.4) at a flow rate of 3-5        ml/min.    -   2. Loading of the total lysate (with wanted fusion protein) on        the Histrap FF 5 ml column at a flow rate of 3-5 ml/min.    -   3. Washing of the column with up to 10 column volumes of Washing        Buffer to remove unbound sample followed by a second washing        step with 10% Elution buffer (500 mM imidazole, 0.5 M NaCl and        20 mM Hepes on pH 7.4) at a flow rate of 3-5 ml/min.    -   4. Elution of bounded fusion proteins from the column with a        linear gradient of 4 column volumes of Elution Buffer (500 mM        imidazole, 0.5 M NaCl and 20 mM Hepes on pH 7.4) to 100% at a        flow rate of 3-5 ml/min.

Purified stock solutions of fusion proteins in Elution Buffer (20 mMHepes pH 7.4; 0.5 M NaCl; 500 mM imidazole) were at least 90% pure asdetermined visually on SDS-PAGE gels (data not shown).

EXAMPLE 4: ANTIMICROBIAL ACTIVITY OF THE ENDOLYSIN KZ144 MODIFIED WITHVARIOUS PEPTIDE STRETCHES ON THE N-TERMINUS

The fusion protein consisting of KZ144 and the peptide stretch α4 helixwas constructed as described in example 1. The other fusion proteinsconsisting of KZ144 and the respective peptide stretches wereconstructed as described in example 3.

E. coli DSMZ 11753, Acinetobacter baumannii DSMZ 30007 and Pseudomonasaeruginosa PAO1p cells (Burn wound isolate, Queen Astrid Hospital,Brussels; Pirnay J P et al. (2003), J Clin Microbiol., 41(3):1192-1202)were used as test strains. Overnight cultures were diluted 10-fold infresh LB medium and grown to OD₆₀₀=0.6. The culture was spun down anddiluted 10-fold in dilution buffer (10 mM HEPES, 0.5 mM EDTA; pH 7.4).Bacteria were incubated at room temperature with each 10 μg undialyzedfusion protein at a final concentration of 100 μg/ml in buffer (20 mMNaH₂PO₄—NaOH pH 7.4; 0.5 M NaCl; 0.5 M imidazole). After 1 hour celldilution series were made in PBS and plated on LB. Additionally, anegative control was plated using buffer (20 mM NaH₂PO₄—NaOH pH 7.4; 0.5M NaCl; 0.5 M imidazole). The residual colonies were counted after anovernight incubation at 37° C. Based on the counted cell numbers theantibacterial activity as logarithmic units (=log₁₀N₀/N_(i) withN₀=number of untreated cells and N_(i)=number of treated cells) wascalculated (Table 11). All samples were replicated at least in fourfold.

The antimicrobial activity of these fusion proteins is given in thefollowing table.

TABLE 11 Antimicrobial activity of KZ144 modified with various peptidestretches against gram-negative bacteria Activity against Peptidestretch Activity against Activity against Acinetobacter (N-terminalunless Pseudomonas E. coli baumannii Fusion protein Enzyme partotherwise indicated) aeruginosa DSMZ 11753 DSMZ 30007 SEQ ID NO: 77KZ144 Pseudin 1 + n.d. n.d. (SEQ ID NO: 25) (SEQ ID NO: 29) SEQ ID NO:78 KZ144 Ranalexin + n.d. n.d. (SEQ ID NO: 25) (SEQ ID NO: 30) SEQ IDNO: 79 KZ144 Sushi 1 + n.d. ++ (SEQ ID NO: 25) (SEQ ID NO: 32) SEQ IDNO: 80 KZ144 WLBU2-Variant n.d. + n.d. (SEQ ID NO: 25) (SEQ ID NO: 33)SEQ ID NO: 81 KZ144 Melittin + n.d. n.d. (SEQ ID NO: 25) (SEQ ID NO: 31)SEQ ID NO: 82 KZ144 SMAP-29 +++ +++ n.d. (SEQ ID NO: 25) (SEQ ID NO: 11)SEQ ID NO: 83 KZ144 Cecropin A (A. ++ + ++ (SEQ ID NO: 25) aegypti) (SEQID NO: 14) SEQ ID NO: 84 KZ144 Pleurocidin + n.d. n.d. (SEQ ID NO: 25)(SEQ ID NO: 6) SEQ ID NO: 85 KZ144 Cecropin A (A. + n.d. n.d. (SEQ IDNO: 25) melanogaster) (SEQ ID NO: 15) SEQ ID NO: 86 KZ144 Buforin II +n.d. n.d. (SEQ ID NO: 25) (SEQ ID NO: 8) SEQ ID NO: 87 KZ144 SarcotoxinIA ++ ++ ++ (SEQ ID NO: 25) (SEQ ID NO: 16) SEQ ID NO: 93 KZ144 α4 helix± n.d. n.d. (SEQ ID NO: 25) (SEQ ID NO: 92) Abreviations: ± <1 log; +: 1log; ++: 2-3 log; +++: 4 or more logs; n.d. means that this strain wasnot tested with the respective fusion protein.

EXAMPLE 5: ANTIMICROBIAL ACTIVITY OF THE ENDOLYSIN STM0016 MODIFIED WITHVARIOUS PEPTIDE STRETCHES ON THE N-TERMINUS

The fusion proteins consisting of STM0016 and the peptide stretchSarcotoxin IA or SMAP-29 was constructed as described in example 3.

E. coli DSMZ 11753, Salmonella typhimujrium DSMZ 17058 and Pseudomonasaeruginosa PAO1p cells (Burn wound isolate, Queen Astrid Hospital,Brussels; Pirnay J P et al. (2003), J Clin Microbiol., 41(3):1192-1202)were used as test strains. The antimicrobial activity of the fusionproteins consisting of the endolysin STM0016 and the peptide SarcotoxinIA or SMAP-29 was examined as described in example 4. The antimicrobialactivity of these fusion proteins is given in the following table.

TABLE 12 Activity against Peptide stretch Activity against Activityagainst Salmonella (N-terminal unless Pseudomonas E. coli typhimuriumFusion protein Enzyme part otherwise indicated) aeruginosa DSMZ 11753DSMZ 17058 SEQ ID NO: 88 STM0016 Sarcotoxin IA + n.d. + (SEQ ID NO: 22)(SEQ ID NO: 16) SEQ ID NO: 89 STM0016 SMAP-29 + + + (SEQ ID NO: 22) (SEQID NO: 11) Abreviations: +: 1 log; n.d. means that this strain was nottested with the respective fusion protein.

EXAMPLE 6: ANTIMICROBIAL ACTIVITY OF THE ENDOLYSIN N4GP61 MODIFIED WITHA PEPTIDE STRETCH ON THE N-TERMINUS

The fusion protein consisting of N4gp61 and the peptide stretch SMAP-29was constructed as described in example 3.

E. coli DSMZ 11753, Salmonella typhimujrium DSMZ 17058 and Pseudomonasaeruginosa PAO1p cells (Burn wound isolate, Queen Astrid Hospital,Brussels; Pirnay J P et al. (2003), J Clin Microbiol., 41(3):1192-1202)were used as test strains. The antimicrobial activity of the fusionprotein consisting of the endolysin N4gp61 and the peptide SMAP-29 wasexamined as described in example 4. The antimicrobial activity of thisfusion protein is given in the following table.

TABLE 13 Activity against Peptide stretch Activity against Activityagainst Salmonella (N-terminal unless Pseudomonas E. coli typhimuriumFusion protein Enzyme part otherwise indicated) aeruginosa DSMZ 11753DSMZ 17058 SEQ ID NO: 90 N4-gp61 SMAP-29 + + + (SEQ ID NO: 23) (SEQ IDNO: 11) Abreviations: +: 1 log; n.d. means that this strain was nottested with the respective fusion protein.

EXAMPLE 7: ANTIMICROBIAL ACTIVITY OF THE ENDOLYSIN GP188 MODIFIED WITH APEPTIDE STRETCH ON THE N-TERMINUS

The fusion proteins consisting of the endolysin gp188 and the peptidestretches α4 helix, SMAP-29 or Sarcotoxin IA were constructed asdescribed in example 1. E. coli DSMZ 11753, Acinetobacter baumannii DSMZ30007 and Pseudomonas aeruginosa PAO1p cells (Burn wound isolate, QueenAstrid Hospital, Brussels; Pirnay J P et al. (2003), J Clin Microbiol.,41(3):1192-1202) were used as test strains. The antimicrobial activityof the fusion proteins consisting of the endolysin gp188 and therespective peptide stretches was examined as described in example 4. Theantimicrobial activity of these fusion proteins is given in thefollowing table.

TABLE 14 Activity against Peptide stretch Activity against Activityagainst Acinetobacter (N-terminal unless Pseudomonas E. coli baumanniiFusion protein Enzyme part otherwise indicated) aeruginosa DSMZ 11753DSMZ 30007 SEQ ID NO: 94 gp188 α4 helix ± n.d. n.d. (SEQ ID NO: 2) (SEQID NO: 92) SEQ ID NO: 95 gp188 SMAP-29 ++ ++ ++ (SEQ ID NO: 2) (SEQ IDNO: 11) SEQ ID NO: 96 gp188 Sarcotoxin IA + + + (SEQ ID NO: 2) (SEQ IDNO: 16) Abreviations: ± <1 log; +: 1 log; ++: 2-3 log; n.d. means thatthis strain was not tested with the respective fusion protein.

EXAMPLE 8: ANTIMICROBIAL ACTIVITY OF THE SALMONELLA ENDOLYSIN MODIFIEDWITH THE PEPTIDE STRETCH SMAP-29 ON THE N-TERMINUS

The fusion proteins consisting of the Salmonella endolysin having anamino acid sequence according to SEQ ID NO: 3 and the peptide stretchSMAP-29 were constructed analogous to example 3. E. coli DSMZ 11753 andSalmonella typhimurium DSMZ 17058 were used as test strains. Theantimicrobial activity of the fusion protein was examined as describedin example 4. The antimicrobial activity of this fusion protein is givenin the following table.

TABLE 15 Activity against Peptide stretch Activity against Salmonella(N-terminal unless E. coli typhimurium Fusion protein Enzyme partotherwise indicated) DSMZ 11753 DSMZ 17058 SEQ ID NO: 97 SalmonellaSMAP-29 + + endolysin (SEQ ID NO: 11) (SEQ ID NO: 3) Abreviations: +: 1log;

EXAMPLE 9: ANTIMICROBIAL ACTIVITY OF THE ACINETOBACTER BAUMANNIIENDOLYSIN MODIFIED WITH VARIOUS PEPTIDE STRETCHES ON THE N-TERMINUS

The fusion proteins consisting of the Acinetobacter baumannii endolysinhaving an amino acid sequence according to SEQ ID NO: 5 and the peptidestretches SMAP-29, Pseudin 1 and Sushi 1 were constructed analogous toexample 3. Acinetobacter baumannii DSMZ 30007 and Pseudomonas aeruginosaPAO1p cells (Burn wound isolate, Queen Astrid Hospital, Brussels; PirnayJ P et al. (2003), J Clin Microbiol., 41(3):1192-1202) were used as teststrains. The antimicrobial activity of the fusion proteins was examinedas described in example 4. The antimicrobial activity of these fusionproteins is given in the following table.

TABLE 16 Activity against Peptide stretch Activity against Acinetobacter(N-terminal unless Pseudomonas baumannii Fusion protein Enzyme partotherwise indicated) aeruginosa DSMZ 30007 SEQ ID NO: 98 AcinetobacterPseudin 1 ± n.d. baumannii (SEQ ID NO: 29) endolysin (SEQ ID NO: 5) SEQID NO: 99 Acinetobacter SMAP-29 ++ ++ baumannii (SEQ ID NO: 11)endolysin (SEQ ID NO: 5) SEQ ID NO: 100 Acinetobacter Sushi 1 + +baumannii (SEQ ID NO: 32) endolysin (SEQ ID NO: 5) Abreviations: ± <1log; +: 1 log; ++: 2-3 log; n.d. means that this strain was not testedwith the respective fusion protein.

The fusion proteins in Table 11 to 16 without any tag and linker werealso tested with the activity assays described above. They all showedantimicrobial activity against the used bacterial strains (data notshown).

The invention claimed is:
 1. A fusion protein comprising an endolysinhaving the activity of degrading the cell wall of Gram-negative bacteriaand a peptide segment fused to the endolysin at the N- or C-terminus orat both termini, wherein the peptide segment is a cathelicidine or amagainine.
 2. The fusion protein according to claim 1, wherein thepeptide segment consists of about 12 to about 100 amino acid residues.3. The fusion protein according to claim 2, wherein the peptide segmentconsists of about 12 to 50 amino acid residues.
 4. The fusion proteinaccording to claim 2, wherein the peptide segment consists of about 12to 30 amino acid residues.
 5. The fusion protein according to claim 1,wherein said fusion protein comprises an additional amino acid residueon the N-terminus.
 6. The fusion protein according to claim 1, whereinsaid fusion protein comprises a tag or additional protein on the C-and/or N-terminus.
 7. The fusion protein according to claim 1, whereinthe peptide segment is linked to the endolysin by one or more additionalamino acid residues.
 8. The fusion protein according to claim 1, whereinthe endolysin comprises an amino acid sequence according to any of SEQID NO: 1, 2, 3, 4, 5, 18, 20, 21, 22, 23, 24, 25 or
 34. 9. The fusionprotein according to claim 1, wherein the peptide segment comprises anamino acid sequence according to any of SEQ ID NO: 9, 10, 11, 12, or 13.10. The fusion protein according to claim 1, wherein the Gram-negativebacteria are selected from the group consisting of: Enterobacteriaceae,Pseudomonadaceae, Neisseria, Moraxella, Vibrio, Aeromonas, Brucella,Francisella, Bordetella, Legionella, Bartonella, Coxiella, Haemophilus,Pasteurella, Mannheimia, Actinobacillus, Gardnerella, Spirochaetaceae,Leptospiraceae, Campylobacter, Helicobacter, Spirillum, Streptobacillus,Bacteroidaceae and Acinetobacter.
 11. The fusion protein according toclaim 10, wherein the Gram-negative bacteria are selected from the groupconsisting of Escherichia, Salmonella, Shingella, Citrobacter,Edwardsiella, Enterobacter, Hafnia, Klebsiella, Moganella, Proteus,Providencia, Serratia, Yersinia, Pseudomonas, Burkholderia,Stenotrophomonas, Shewanella, Sphingomonas, Comamonas, Treponema,Borrelia, Bacteroides, Fusobacterium, Prevotella, Porphyromonas and A.baumanii.
 12. An isolated nucleic acid molecule encoding a fusionprotein according to claim
 1. 13. A vector comprising the nucleic acidmolecule according to claim
 12. 14. A host cell comprising the nucleicacid molecule according to claim 12 or the vector according to claim 13.15. The host cell according to claim 14, wherein the cell is a bacterialcell or a yeast cell.
 16. A pharmaceutical composition comprising afusion protein according to claim
 1. 17. A fusion protein comprising anendolysin having the activity of degrading the cell wall ofGram-negative bacteria and a peptide segment fused to the endolysin atthe N- or C-terminus or at both termini, wherein the peptide segmentcomprises SEQ ID NO: 33.